Crop productivity per unit area is a function of both available resources and how those resources are partitioned. The relative distribution of energies to different portions of the growing plant determines the proportion of useful biomass in the crop. This is referred to as the “harvest index”. The pattern of resource allocation is plastic and can be regulated in response to changing environmental conditions, such as light and nutrient availability. However, adaptive competition strategies that have evolved through natural selection may be at odds with the agronomic performance of cultivated plants. The response exhibited by plants to competing vegetation has been termed “shade-avoidance”, and is characterized by increased stem elongation, decreased leaf expansion, and precocious reproductive development. Smith, H., “Physiological and Ecological Function Within the Phytochrome Family,” Ann. Rev. Plant Physiol.—Plant Mol. Biol. 46:289-315 (1995). The onset of shade avoidance is triggered by changes in the light environment caused by surrounding vegetation. Full sunlight contains equal fluxes of red light (“R”) and far-red light (“FR”). Holmes et al., “The Function of Phytochrome in Plants Growing in the Natural Environment,” Nature 254:512-514 (1975). However, when light filters through a crop canopy, the majority of R is either reflected or absorbed. Cumming, B., “The Dependence of Germination on Photoperiod, Light Quality and Temperature in Chenopodium sp.,” Can. J Bot. 41:1211-1233 (1963). As a consequence, the ratio of R:FR falls from approximately 1 in incident sunlight, to approximately 0.2 at ground level. Holmes et al., “The Function of Phytochrome in Plants Growing in the Natural Environment,” Nature 254:512-514 (1975). Plants use this change in R:FR ratio to monitor the proximity of local vegetation. Holmes et al., “The Function of Phytochrome in Plants Growing in the Natural Environment,” Nature 254:512-514 (1975); Holmes et al., “The Function of Phytochrome in the Natural Environment IV, Light Quality and Plant Development,” Photochem. Photobiol. 25:551-557 (1977). Although plants possess a number of photoreceptor systems that might mediate neighbor perception, genetic and physiological analyses have demonstrated that changes in R:FR ratio are primarily detected by members of the phytochrome family. Quail et al., “Phytochromes: Photosensory Perception and Signal Transduction,” Science 268:675-680 (1995); Smith, H., “Phytochromes and Light Signal Perception by Plants—An Emerging Synthesis,” Nature 407:585-591 (2000); Nagy et al., “Phytochromes Control Photomorphogenesis by Differentially Regulated, Interacting Signaling Pathways in Higher Plants,” Annu. Rev. Plant Biol. 53:329-355 (2002).
The phytochromes are the best characterized family of photoreceptors, mediating many of the plant responses to changes in their light environment. Quail, P., “Phytochrome Photosensory Signaling Networks,” Nat. Rev. Mol. Cell Biol. 3:85-93 (2002). In Arabidopsis thaliana, the phytochrome family consists of five genes: phytochrome A (“PHYA”), phytochrome B (“PHYB”), phytochrome C (“PHYC”), phytochrome D (“PHYD”), and phytochrome E (“PHYE”). Clack et al., “The Phytochrome Apoprotein Family in Arabidopsis is Encoded by Five Genes: The Sequences and Expression of PHYD and PHYE,” Plant Mol. Biol. 25:413-427 (1994). In grasses, including rice, the family consists of only three members: PHYA, PHYB and PHYC. Dehesh et al., “PHYB is Evolutionarily Conserved and Constitutively Expressed in Rice Seedling Shoots,” Mol. Gen. Genet. 225:305-313 (1991); Mathews et al., “The Phytochrome Gene Family in Grasses (Poaceae): A Phylogeny and Evidence That Grasses Have a Subset of the Loci Found in Dicot Angiosperms,” Mol. Biol. Evol. 13:1141-1150 (1996). The basis of phytochrome action is the reversible photoconversion between a red light absorbing form (“Pr”) and a far-red absorbing form (“Pfr”). Quail, P., “Phytochrome Photosensory Signaling Networks,” Nat. Rev. Mol. Cell Biol. 3:85-93 (2002). Although this mechanism is common to all phytochromes, genetic analyses in Arabidopsis have shown that PHYA and PHYB have both distinct and overlapping roles during plant development. Whitelam et al., “Phytochrome A Null Mutants of Arabidopsis Display a Wild-type Phenotype in White Light,” Plant Cell 5:757-768 (1993); Nagatani et al., “Isolation and Initial Characterization of Arabidopsis Mutants that are Deficient in Phytochrome A,” Plant Physiol. 102:269-277 (1993).
Functional divergence between PHYA and PHYB is due, in part, to differences in Pfr stability. Quail, P., “Phytochrome Photosensory Signaling Networks,” Nat. Rev. Mol. Cell Biol. 3:85-93 (2002). PHYA is rapidly degraded following conversion of Pr to Pfr, and it is most abundant prior to de-etiolation. Clough et al., “Phytochrome Degradation,” Plant Cell Environ. 20:713-721 (1997). In contrast, PHYB is relatively light stable in both Pr and Pfr forms, and accumulates as the principal phytochrome in mature plants. Wagner et al., “Overexpression of Phytochrome B Induces a Short Hypocotyl Phenotype in Transgenic Arabidopsis,” Plant Cell 3:1275-1288 (1991). PHYB mutants of Arabidopsis show a weak response to reductions in the R:FR ratio, and PHYB has been assigned a major role in the induction of the shade avoidance response. Whitelam et al., “Retention of Phytochrome-mediated Shade Avoidance Responses in Phytochrome-deficient Mutants of Arabidopsis, Cucumber, and Tomato,” J. Plant Physiol. 139:119-125 (1991).
In view of the light-labile nature of PHYA, one of the more surprising results of genetic analyses has been the demonstration that PHYA is required for the normal development of light-grown plants. Johnson et al., “Photoresponses of Light-grown PHYA Mutants of Arabidopsis,” Plant. Physiol. 105:141-149 (1994). Interestingly, PHYA plays a role in the regulation of plant architecture that appears to be antagonistic to that of PHYB. In a characterization of seedling growth, PHYA mutants of Arabidopsis displayed an exaggerated response to a reduction in the R:FR ratio, while transgenic tobacco plants expressing high levels of an oat PHYA displayed reduced sensitivity to changes in the R:FR ratio. Casal, J., “Phytochrome A Enhances the Promotion of Hypocotyl Growth Caused by Reductions in Levels of Phytochrome B in its Far-red-light-absorbing Form in Light-grown Arabidopsis thaliana,” Plant Physiol. 110:965-973 (1996). In contrast, PHYA mutants of japonica rice (Nipponbare) did not show noticeable morphological changes in mature rice plants even though the expression pattern of chlorophyll a/b-binding proteins (“CAB”) and small subunit of the Rubisco (“RbcS”) was slightly altered. Takano et al., “Isolation and Characterization of Rice Phytochrome A Mutants,” Plant Cell 13:521-534 (2001). Similarly, overexpression of rice PHYA partially complemented PHYB deficiency in Arabidopsis, but did not restore responses to low R:FR ratio. Halliday et al., “Overexpression of Rice Phytochrome A Partially Complements Phytochrome B Deficiency in Arabidopsis,” Planta 207:401-409 (1999). Thus, precise roles for PHYA and PHYB in regulating mature plant development have been difficult to ascertain.
In recent years, shade avoidance has become a target of genetic modification of plants with the expectation that a reduction in the response may have positive effects upon yield. Based upon the characterization of light-signaling in Arabidopsis, these attempts have aimed to use the transgenic over-expression of PHYA to inhibit the action of PHYB. Clough et al., “Expression of a Functional Oat Phytochrome A in Transgenic Rice.” Plant Physiol. 109:1039-1045 (1995); Robson et al., “Genetic Engineering of Harvest Index in Tobacco Through Overexpression of a Phytochrome Gene,” Nat. Biotechnol. 14:995-998 (1996). Clough et al. successfully expressed an oat PHYA in rice under the control of the cauliflower mosaic virus (CaMV) 35S promoter, and detected a four-fold increase in total phytochrome activity in light-grown transgenic lines. However, under standard growth conditions, the phenotype of mature transgenic rice plants was indistinguishable from that of non-transgenic plants. Clough et al. concluded that a larger increase in the level of PHYA would be required to significantly alter the phenotype of the transgenic rice or that the japonica rice (Gulfinont) used in their study may be insensitive to increased PHYA levels.
Rice is the staple food for more than half of the world's population and therefore, stands as the world's most agronomically important crop. Indica rice varieties, including aromatic rices, represent 80% of rice grown worldwide. Aromatic rice varieties, including Basmati rice, are characterized by exquisite aroma and grain quality. Rani et al., “Current Status and Future Prospects for Improvement of Aromatic Rices in India,” in Chaudhary et al., eds., Specialty Rices of the World: Breeding Production and Marketing, Science Publishers, Inc., Enfield, N.H., USA, pp. 49-78 (2000), and receive a premium price in global agricultural markets. Bhasin, V., “India and the Emerging Global Rice Market,” in Singh et al., eds., Aromatic Rices, Science Publishers, Inc., Enfield, N.H., USA, pp. 257-276 (2000).
To date, however, it has been difficult to improve traditional Basmati cultivars into high yielding “elite” Basmati evolved lines by conventional rice breeding. This is mainly due to the complex nature of quality traits and the association of undesirable traits of Basmati, such as its tall stature, low yield, weak-stem and droopy leaves, sensitivity to photoperiod, and poor response to fertilizer. Khush et al., “Developing Basmati Rices with High Yield Potential,” in Chaudhary et al., eds., Specialty Rices of the World: Breeding Production and Marketing, Science Publishers, Inc., Enfield, N.H., USA, pp. 49-78 (2000).; Rani et al., “Current Status and Future Prospects for Improvement of Aromatic Rices in India,” in Chaudhary et al., eds., Specialty Rices of the World: Breeding Production and Marketing, Science Publishers, Inc., Enfield, N.H., USA, pp. 49-78 (2000). Hence, the development of genetically engineered Basmati plants with improved agronomic characteristics presents a current challenge in crop biotechnology.
The present invention is directed to overcoming these and other deficiencies in the art.